Stargate: Return of the Ancients, Pilot Episode
by Aer-ki Jyr
Summary: After Season 5 conclusion... a pilot episode for what would be both a new series and a continuation of Stargate Atlantis. Assuming Enemy at the Gate never happened. Wormhole drive my eye!
1. Chapter 1

"I regret it's come to this, Colonel. To be completely honest, I've always admired you…but now you've crossed a line that I simply cannot condone," Woolsey said with a tone of finality as he and Sheppard stood in front of the gate in Atlantis's control room. An active wormhole back to Earth shimmered ominously large in front of them.

"You're breaking my heart," John said sarcastically as Ronon eyed him from afar. He knew his friend was spoiling for a fight, and subtly waved him off with a downward flick of his bound wrists.

Ronon sneered in disgust, but his movements seemed to settle down. He knew there was nothing that he could do for Sheppard, but that didn't mean he wasn't willing to go down fighting for his friend.

"If there was any way to make this more pleasant for you, I would…"

"How about I punt your dishonorable ass back through the gate instead," Sheppard countered, clearly agitated.

Woolsey stiffened. "You can rest assured that will not be happening." He purposefully turned and looked at the open gate. "Once you step through that gate I doubt you'll ever lay eyes on one again. I hope it was worth it for you." Woolsey nodded to the security guards. "Send him through."

The SFs took Sheppard by the elbow and dragged him forward.

"John!" Teyla yelled out, not knowing what else to say...or do.

Sheppard dug his heels into the ground three feet from the puddle and turned to look back at her. He gave her an unconvincing smile before he was dragged into the event horizon.

* * *

"Donnor, Davis, watch the gate," Colonel Morris barked out a few minutes after SG-14 arrived on the previously unexplored world through the stargate for the second time in three days…this time with an archeology team in tow. "Stevenson, you and me are on patrol. Take the southern ruins that we didn't get to last time, I'll take the plaza then escort the egg heads around. Report anything interesting."

"Roger that," Stevenson said, turning south through the decaying remains of an Ancient city. Though mostly made up of abandoned buildings and crumbling infrastructure, a few pieces of ancient tech had been discovered on their first trip through the gate.

Nothing groundbreaking had been found, but the fact that some tech remained suggested that the planet hadn't been scavenged by the Goa'uld or others…and that meant there might still be something worthwhile lying around.

Captain Ryan Stevenson, fresh off a stint with SG-7, had been reassigned less than a week ago after personally requesting General Landry to move him to one of the teams tasked with exploring the remaining gates on the SGC's galactic list that General O'Neill had provided them with years ago. After an hour of debate, and a check of his medical records, Landry somberly granted his request and moved him into an open slot on an exploration team that a recently pregnant Lieutenant had vacated.

After half an hour of meandering through the ruins with nothing but rubble to report, Stevenson checked in on his radio and headed back to the main structure where the stargate was located. It was one of the few worlds that the Humans had explored that had the gate indoors, which suggested to the experts back in the SGC that the planet might hold a greater significance than other Ancient sites previously discovered.

There was even some scuttlebutt back in the SGC about establishing a permanent base in the ruins. While some of the buildings seemed intact to Stevenson, they weren't what he'd call livable. Most had holes of some sort in them, and the oppressive jungle surrounding the site had managed to invade every crack and crevice that it could, creating a hybrid city/forest that would require camping equipment in order to inhabit.

But that didn't really matter to him. He and his team would be moving on to the next address on the diminishing unexplored list within a few days. He hoped they'd be able to finish off the uncharted gates in the Milky Way before he was deemed unfit for duty.

Stevenson wound his way through the western edge of the ruins that he'd spied from afar earlier. There were several statues and large columns that seemed slightly out of place from the rest of the structures. They were clearly Ancient in design, but their coloration and placement suggested they weren't part of the original architecture.

As he walked down a wide corridor and past the foot of one large female statue Stevenson jerked his P-90 up in response to movement on his flank.

He lowered the weapon when he recognized the source…a section of the pedestal had jutted out towards him.

A memory from his initial SGC training clicked and he reached for his radio. General O'Neill had encountered this technology twice during his tour on SG-1.

Stevenson's finger froze over the radio's call button as another thought struck him. He felt a flicker of hope bristle through his skin before his mind quickly dismissed the illogic of it. O'Neill had nearly died both times.

Without thinking his hand retreated from his radio. He looked down at it in wonder, realizing his instincts were disagreeing with his logic. Stevenson looked up at the partially deployed Ancient Repository of Knowledge and swallowed hard.

"I'm dead anyway," he said to himself. "Million to one is better than no odds at all."

Stevenson pulled the green cap off his head and closed his eyes. He sucked in one last breath and stepped forward.


	2. Chapter 2

"You've really done it this time, Sheppard," Landry said from across the table in the brig.

"Done what, exactly?" Sheppard asked innocently.

"Done what?" Landry repeated for emphasis. "Well, let's start with the obvious. Disobeying orders. I specifically ordered you and your teams not to go on any further offworld missions. The I.O.A. doesn't want us to needlessly jeopardize any more of our personnel fighting the Wraith when we know that any gains made will be for naught when we pull out of Pegasus."

"So we just turn tail and run because the Wraith are proving more resilient than the Goa'uld did?" Sheppard argued loudly.

Landry leaned his elbows over the table and looked Sheppard directly in the eye. "The original purpose of the Atlantis expedition was to recover Ancient technologies and bring them back to Earth…which is exactly what we're doing now. Fighting the Ancients' millennia old war is not why you were sent there…and despite the relationships you've established with the indigenous Humans in the Pegasus galaxy, their wellbeing is ultimately not our concern. And you, Colonel Sheppard, have no right to unilaterally inject Earth into the conflict."

Sheppard leaned forward as well. "Are you referring to recent events, or the original rescue mission that woke up the Wraith?"

"Both points could be argued, but I was referring to your recent assault on the Wraith outpost."

"They were setting up a new shipyard," Sheppard argued, "one that could grow ships that could be used to attack Earth in the future."

"The I.O.A. disagrees. It feels that without the advanced, intergalactic hyperdrive technology the Wraith will stay confined to the Pegasus galaxy the same way they have been for the past 10,000 years…and I'm forced to agree with them."

"So let me get this straight," Sheppard said quizzically. "I'm being court-martialled because I disobeyed orders and succeeded in thwarting the Wraith's attempt to build more ships that could be used to attack Atlantis during the pullout? I thought that sort of thing usually led to a commendation, or at least an informal pat on the back."

Landry shook his head. "It doesn't matter how it turned out, Colonel. You're a loose cannon and the I.O.A. has had it with your independent streak…as have I. Don't think that I haven't noticed certain supplies that have been mysteriously expended at a rate far faster than previous logistical reports."

Sheppard cringed.

"Oh…I see you didn't realize that. You thought you were real clever, ordering ammo, and weapons, and medical supplies through channels and then slipping them out of Atlantis's inventory in small numbers that wouldn't raise any suspicion."

"One good thing I'll say about Woolsey is that he's efficient," Landry continued. "He's the one that spotted the questionable figures. Don't care much for the man myself, but you've gotta respect that kind of obsessive scrutiny when it leads to the capture of a thief."

That brought Sheppard's ire up. "I'm no thief!"

"Oh no?" Landry said, standing up suddenly. "Then who was it that cooked the books? McKay? Lorne? Or was it Teyla's idea?"

"You know…" Sheppard said, shaking his head in disgust. "I thought Earth was supposed to be the good guy. The one the galaxy…or galaxies could turn to in times of trouble. Like the way the Asgard came to our aid when the Goa'uld were set to wipe us out."

"Oh, we're still the good guys, Colonel. But sometimes the good guys have to cut their losses and look out for themselves. Even the Asgard came to the same conclusion when the Replicators were killing them off. They chose, and rightly so, to protect their own first. Fortunately it worked out for Earth and we were able to defend ourselves from the Goa'uld at that point."

"We're not under attack," Sheppard countered, "so we aren't in a position to have to make that choice. We're just leaving for…why are we leaving anyway?"

"Because, frankly, it's none of our business what happens in Pegasus. We're not going to throw away the lives of our people in a hopeless effort to defeat the Wraith."

"It's not hopeless, General. The Wraith are tough but they aren't unbeatable."

"Apparently the Ancients didn't think so, and while I'm not the kind to back down from a fight, I think we'll take their word over yours as to how dangerous the Wraith really are. By your own accounts, Atlantis has survived this far purely out of luck, with a little hard work and courage thrown into the mix. If the Wraith find Atlantis again, they'll destroy the city through sheer numbers and there's nothing that we can do to fend them off. If the Ancients couldn't beat them then what chance in hell do we have?"

"Fine," Sheppard offered. "Let's hold out long enough to evacuate the Human populations from Pegasus back into the Milky Way. The Wraith have kept their numbers low, and without a food source the Wraith will either have to find something else to eat or starve to death."

Landry held his tongue for a moment. "There at least I can sympathize. While I don't expect that we could evacuate an entire galaxy, we could at least provide refuge for some of the Humans civilizations that we've befriended. I don't like turning our backs on our allies any more than you do, Colonel, but the I.O.A. is ultimately the one in charge. And like it or not, we have to follow orders."

"Even if they're bad orders?"

"Even if they're bad ones, Colonel. You've had too much leniency in Pegasus for your own good. Being a galaxy away from command influence probably didn't help matters any. I'll be sure to bring that point up at your court-martial," Landry said as he turned to leave.

"That's it?" Sheppard asked. "You just stopped in to chat?"

"Believe it or not, Colonel, I have another disobedient soldier to deal with…or perhaps not. I doubt he'll live out the month. He's probably better off, given the circumstances."

"What happened?" Sheppard asked. "Did Ronon do something?"

"No, Colonel. He's one of mine. Seems he found an Ancient Repository and decided to use it on himself."

"What's an Ancient Repository?"

"General O'Neill refers to it as a 'head sucker'. Thing is it nearly killed him…twice. The Asgard saved his life both times, but Captain Stevenson won't have that luxury."

"Did he know it'd kill him?" Sheppard asked.

"Probably," Landry offered, "Only he knows for sure, and right now he's in a coma in sickbay. Seems he disobeyed orders and didn't report it in. His team leader found him unconscious beneath the device."

"How do you know he did it on purpose?"

"Standing up for another rogue…how touching," Landry said sarcastically. "We found his hat several meters away from the device, along with some very distinctive footprints. He didn't just walk by and it grabbed him. Apparently he took his hat off before walking straight up to it and sticking his head in. Either way I'll find out for sure when he wakes up. I've got Dr. Jackson standing by to translate."

"Translate?" Sheppard asked, confused.

"Seems the Repository rewrites your brain with Ancient knowledge. General O'Neill eventually lost the ability to speak English."

Landry opened the confinement room door. "If I were you I'd start planning your defense. Your designated council will be here in the next hour, but you're going to need as much prep time as you can get. If I weren't ticked with you I'd wish you luck, even though I know it wouldn't do you any good. You're going to be staring at the inside of a cell for most, if not all of your remaining life."

Landry shut the door behind him with a clank, leaving Sheppard sitting alone behind the spartan table with the security guard watching over him from the corner.

Sheppard turned to look over his shoulder at the female guard. "Do we get any bathroom breaks?"


	3. Chapter 3

"Has he said anything?" Dr. Lam asked Daniel when she returned to Stevenson's bed after taking a brief lunch.

"He woke up for about thirty seconds, complained about a headache, and passed out again."

"In English?" she asked.

"Yep," he answered, then shook his head in disbelief. "Why would he do this knowing that it was going to kill him?"

Lam looked at him quizzically. "You don't know?"

Daniel stared at her. "Know what?"

She hesitated. "I'm not exactly supposed to reveal personal information, but I guess it won't hurt in this case. You probably need to know anyway if you're going to be talking to him. He has a degenerative genetic disease. He's not expected to live more than three more years."

Daniel turned back and looked at Ryan. "I didn't know that."

"He wanted it kept a secret, and I was ethically forced to oblige as long as his illness didn't disqualify him from duty."

"How could it not?" Daniel asked.

Lam shrugged. "As long as he can handle the pain and carry out his daily tasks there's no medical reason to take him off the active duty list. His disease moves slowly, it's not like it's going to develop to a critical level during a mission. He'll slowly be subjected to more and more pain until he can't take it any longer or his superiors notice a physical inability. He said he didn't want them to know so that they wouldn't pull him off duty without reason."

"I grudgingly agreed and have waited for a medical incident to indicate he was no longer fit for duty, but so far that hasn't happened. Either his condition isn't progressing as fast as predicted or he's hiding the pain well. Either way it's a moot point. The Ancient device is going to kill him long before his disease will."

Daniel sighed. "I guess he figured he didn't have anything to lose. Maybe he'll be able to tell us something useful and make his death worth something."

"He made it clear to me he didn't want to die helpless in bed, slowly withering away," Lam confided. "At least this will be quick by comparison."

Suddenly the status monitors started wailing and Stevenson's body began to convulse. Lam reacted instantly and ordered up a cocktail of drugs. "Did this happen to O'Neill?"

"No," Daniel said confused. "His physical deterioration happened after his mental conversion."

"This isn't good," Lam said, alarmed. "His blood pressure is spiking, and his neural patterns are erratic. I don't know how long his body can take this…"

The constant tone of heart failure sounded as Stevenson's body fell still.

"Get the crash cart over here, now!" Lam yelled.

Daniel watched dejectedly as Dr. Lam worked feverishly to revive the Captain, but to no avail. Ten minutes later Lam finally gave up and deactivated the medical equipment. She morosely pulled the bed sheet up over his head and hobbled away from the dead patient.

"There was nothing you could have done," Daniel said, trying to comfort her.

"I know," she said, not happy in the least.

"We knew this would happen, we just didn't think it would be this fast."

"A patient died in my infirmary," she said icily. "I don't like that."

Daniel put a hand on her shoulder supportively. He knew there wasn't anything that he could say to make it right. Losing people was always hard.

* * *

"You really blew it this time, Sheppard," O'Neill said as he paced back and forth across the confinement room.

"With respect, sir, as much as I could use a pep talk, what I really need is an ally who can do something about these ridiculous charges," Sheppard said exasperated. The more days that passed the more he was beginning to lose his patience…and his already limited respect for authority.

Jack shook his head. "I can't get you out of this one, Sheppard. Both the President and the I.O.A. want your head. If you'd just defied the I.O.A.'s orders then maybe I could have done something, but stealing from the Air Force ticked the Commander in Chief off royally. They're going to eat you alive in the hearing tomorrow, then shuttle you off for the official beheading," O'Neill said metaphorically. "Just, tell me. Why'd you have to go and do it?"

"Because it was the right thing to do. And I'd expect you of all people to understand that, General." Sheppard said with a bit of venon in his voice. He felt like he was being betrayed by everyone he'd ever remotely respected back on Earth. He seriously wished he'd gone awol back in Pegasus when he'd had the chance.

"What good did it do?" O'Neill asked. "You've been found out and your operations stopped. Are the people of Pegasus any better off than before? The Wraith are still there and nothing you did was going to stop that. You threw your career away for nothing?"

"At least I'll have a clear conscious when I go to sleep at night. I'll know that I did everything I could to save those people," Sheppard said determinately. "Can you say the same, General?"

"Actually, I can," O'Neill countered half-heartedly. "I fought the I.O.A. on this one, Sheppard...and I fought hard. In the end it didn't change anything. Too many people see the logic in bringing back the technology we've found and destroying the Wraith's one and only route into our galaxy. They don't care about some faceless people they've never met nor ever will meet millions of light-years away…and there's nothing I can say or do that's going to change their mind."

"But you're the one that has to give the final order to destroy Atlantis," Sheppard reminded him.

O'Neill thought about saying something, then stopped and swallowed instead.

"The I.O.A. isn't doing this," Sheppard argued, "we are. They may be giving the orders but we're the ones that have to do the dirty work."

"You won't be, if that's any consolation," O'Neill pointed out.

"Whatever happened to disobeying orders when it was the right thing to do?"

"Ah, yes…the right thing to do," O'Neill said slowly, remembering back.

"I know you've been in this position before, General, and that you did the same thing as me."

"But you got caught, Sheppard!" O'Neill said, half joking, half sarcastic. "If you're going to pull a fast one you've gotta be able to get away with it. Did you really think Woolsey wouldn't notice?"

"I…didn't think about that," Sheppard admitted. "I was too busy worrying about people getting life-sucked by the Wraith to worry about the sleeping monsters among our own people."

O'Neill sighed. "I sympathize, Colonel. I really do. If it was up to me you'd be out bagging more bad guys, but the big wigs have stepped in and taken it out of my hands. And despite my best efforts to convince them to preserve Atlantis, they've decided that the remaining power in our ZPMs is too precious a commodity to waste flying the entire city back here. They'd rather strip it down to the carcass and then blow up the carcass. I'll do what I can for you at the hearing, maybe get them to go easy on the confinement request, but it doesn't look good."

O'Neill started to say something more into the silence, but thought twice about it. Neither he nor Sheppard had anything more to say so he finally, awkwardly got up to leave.

"Why is it that we shoot the bad guys on other planets," Sheppard asked, "but here on Earth they get a free pass?"

"Job security." O'Neill said deadpan as he left.


	4. Chapter 4

The sickbay was blissfully quiet and unoccupied while Dr. Lam wrote up the death certificate for Captain Stevenson on her computer. Suddenly one of the nurses screamed in shock.

"What is it?" Lam yelled as she darted out of her seat and around the corner…where she saw Stevenson's body convulsing again. "What the hell?" she said as she reactivated the medical sensors.

"Call the General," Lam ordered as she held down Stevenson's arm so it wouldn't knock the meds off the nearby tray. "Tell him he needs to get down here now."

* * *

Ten minutes later the General walked into the infirmary in stunned disbelief. "You said he was dead?"

"He was," Lam insisted, "for four hours. Then he just came back…I can't explain it. His vitals are stabilizing, albeit slowly. He's gone through three convulsions in the past ten minutes and each time he comes out of it a little better off than before."

"Explain," Landry demanded.

"I can't," Lam said simply.

"Will he recover?" the General asked.

"If I had to guess, I'd say yes, but I'm really not qualified to give you an answer on this one. I have no idea what's happening to him, but he seems to me to be improving…despite being dead earlier."

"Well this complicates things."

"How so?" Lam asked.

"_If_ he lives," Landry said, stressing the 'if', "what do you think the I.O.A. is going to say about it?"

"I don't catch your meaning."

"If the Captain has the knowledge of the Ancients and lives to keep it…"

"…they'll want to turn him into their personal oracle," she finished.

"Hmmn, 'oracle' is a bit more pleasant than what I was thinking about."

Lam stared at him. "He's still an Air Force officer. They can't just treat him as a piece of property."

"I agree, but that doesn't mean they won't try. I'll have to discuss this with General O'Neill before he leaves. Maybe we can head this one off early…and there's still the matter of how this happened in the first place."

"You don't think it was an accident?" Lam asked.

"I'm guessing he did it on purpose, but anything's possible. Let me know when he's lucid…or if things take a turn for the worse."

* * *

Stevenson lay comatose in his bed, his body motionless aside from the occasional tremor. Daniel and Lam stayed with him as much as they could, waiting for a glimpse of consciousness. Days passed by with no external developments. On the inside, however, was an entirely different story.

His mind was hyper-processing a virtual reality simulation preprogrammed into the Ancient coding that had begun to rewrite his body and mind. He as living out days in a matter of minutes, facing challenge after challenge in a grueling simulation designed to test his worth.

If he failed the test he would never remember having undergone it. He would wake up with the Repository of Ancient Knowledge in his mind, but the additional data cache hidden within the confines of the Repository would self-delete in one final security measure designed to insure that the Ancients' final hope wouldn't be discovered and destroyed before it could take effect.

This, however, was not to take place. Inside the virtual testing chamber Stevenson proved his worth and accepted the mandate given to him by proxy. He knew full well the significance of what he was getting himself into, the Ancients had made sure to give him every chance to decline the burden that was about to be placed on his shoulders.

He woke on the end of a deep breath, blinked his eyes and looked around.

"You're in the infirmary, Captain," Lam said from beside him. "You've been unconscious for over a week. Don't try to move just yet."

"Can you understand us?" Daniel asked from the other side of the bed.

"_Yes, Dr. Jackson. My marbles are still in my head_," Stevenson said…in Ancient.

Lam and Daniel exchanged glances. "It seems a few of them have become a bit scrambled," Daniel explained to Stevenson.

"_How so_?" he asked.

"You're speaking in Ancient," Daniel said, making mouthing motions with his hand.

"_Am I? I hadn't noticed_." He worked his mouth around, thinking about something, then a frustrated expression manifested itself on his blank features. "_I can understand you perfectly, but I can't for the life of me speak English_."

"Yeah…well, we've seen this before with O'Neill. The Ancient Repository seems to overwrite your existing language patterns with its own. Eventually you may not even be able to understand English. In which case I'll be here to translate, so you're not completely cut off from society."

"_I don't think that's going to happen to me, but thanks just the same. Talk to you later_."

"Later? You have somewhere to be?" Daniel asked sarcastically just as Stevenson's eyes rolled up into his lids and he started to convulse again.

* * *

"According to Dr. Lam, Captain Stevenson's body is also changing as a result of his contact with the Ancient device," William Parson said from across the SGC's briefing room table. "From all indications his physiology is altering into a form similar to what we saw from the Anubis creation called Khalek. We squandered a unique opportunity for study then…we're not going to waste another opportunity now."

"So what does the I.O.A. suggest?" Landry asked irreverently. "Confine him to a research lab for the rest of his life? This man is one of our own. He has rights."

"Don't think that we in the I.O.A. haven't considered that angle, but each and every one of our Stargate personnel know and accept the risks involved with exploring the galaxy. Captain Stevenson has essentially been hijacked by alien programming intent on remaking him into an alien. He's not Human anymore, or at least he won't be for very long."

"That's your rational?!" Landry asked, half laughing. "That'll never fly. He's still part of the U.S. military and he's not going anywhere unless I order him to."

"That decision may ultimately not be up to you or your country," Parson said evenly. "Never the less, I'm sure some arrangement can be reached to have him examined here in the SGC. I'm sure your people are as anxious as we are to get access to the Ancient library within his mind. It's a freak of nature that he's survived to this point, and with any luck he'll hold on permanently…but if he doesn't and we've only got a limited amount of time for study, isn't it irresponsible to waste an opportunity such as this while we bicker back and forth about it here and up through the chain of command?"

"Yes, there has been a bit of bickering involved," O'Neill said from the head of the table. "I've got Jackson with him now. If he has anything important to say we'll know about it immediately. We've also got a video feed on him 24/7."

"And I've got the biomed sensor that we took from Anubis's lab hooked up and monitoring him as we speak," Lam added. "We're not missing anything from a medical standpoint."

"I'm pleased to hear that," Parson said. "It'll give us time to discuss any long-term research projects. In the mean time you will be forwarding any data gleamed from him to my office?"

"Of course," Landry said, standing up. Parson nodded to both Generals then left the conference table, briefcase in hand and posse in tow.


	5. Chapter 5

"_Where am I_?" Stevenson asked after waking up from another blackout, still speaking in Ancient.

"They've moved you into confinement," Daniel said from his side.

"_Why_?"

"A little something to do with the fact that you admitted to intentionally sticking your head in the…head sucker."

"_Neural Interface_," Stevenson corrected.

"Right, well it seems you and all SGC exploratory teams were given specific instructions in your indoctrination not to mess with an Ancient Repository if you ever ran across one," Daniel reminded him. "So why did you do it?"

"_Certain death isn't very appealing_," he said sarcastically, though Daniel didn't pick up on that intricacy. His knowledge of the Ancient language was tolerable, but Stevenson was speaking it as if he'd done so his entire life.

"You mean you'd rather take a chance on a long shot instead of waiting around to die from a genetic disease?"

Stevenson stared at him. "_You know about that_?"

Daniel nodded. "They only told me after they brought me in to translate. No one else knows. Actually it's really a moot point now. Dr. Lam says the physical alterations taking place inside you are changing your DNA and have wiped out your disease in the process. It seems your long shot paid off…if you survive the transformation process."

Stevenson blew out a relieved breath. "_Good. I was wondering about that. You can tell Lam that I'm past the worst of it. Each time I black out I'm experiencing an upgrade that requires my body and mind to shut down temporarily_."

Daniel raised an eyebrow. "You know that for a fact, or just guessing?"

"_I know_."

"Really…what else do you know?"

"_What do you mean_?" Stevenson asked.

"Come on, you've got the entire Ancient library stored in your mind. Do you have access to any of the good stuff yet?"

"_Like what_?"

"What about Ancient history? Can you tell me anything new?"

Stevenson started to say something then stopped short. "_Maybe later, Dr. Jackson. I'm still fighting a monster migraine and it requires something of a conscious effort to hold it in check_."

"Alright," Daniel said unconvinced as he stood to leave. "I'll be back to check on you later."

Stevenson waved to him as he left, but followed him with his mind. He felt him stop a few meters outside.

"His physical health is improving and his mind seems stable," Dr. Jackson said to someone in the corridor. Stevenson could feel the other mind but couldn't identify the person.

"But?" the other said. Stevenson heard the voice through Jackson's ears and knew it was familiar…Landry. It was General Landry checking up on him.

"But," Jackson continued, "I think he's holding back."

"Holding back what?" Landry asked.

"I don't know," Daniel admitted. "I'm still impressed by the fact that he's survived this long. When Merlin upgraded me he had to install a failsafe in order to prevent an overload that would eventually kill me. I have no idea how his body is going to be able to stabilize the changes that are happening to him, but he seems confident that he'll make it through."

"Oh he does, does he," Landry said. "It might turn out better for him if he doesn't."

"Meaning what?" Daniel asked.

"The I.O.A.," Landry said simply.

"Oh, not again," Daniel said exasperated.

"I'm afraid so. And there's the little fact that he disobeyed standing orders, which is what created this mess in the first place."

Stevenson released his tenuous mental link. His new abilities were intermittent and unreliable, but he'd been able to hear enough. He knew he was going to have to escape the SGC…but he wasn't ready yet. He was too weak and continuing to black out. A few more days and he might be able to risk it. He'd only get one chance before they realized what he was capable of and implemented additional security measures.

"_Patience_," he reminded himself.

* * *

Sheppard left the hearing demoralized and disillusioned. Good men, men he had respected and trusted in the past had, one by one, sided against him and his actions and fell in line with the I.O.A.'s assertion that what happened in Pegasus didn't matter to Earth and that he had had no right to interfere.

General O'Neill had spoken up on his behalf, suggesting that he be given some leniency since his plans to destroy the Wraith shipyard had actually succeeded and therefore aided the I.O.A.'s plans to withdraw from the Pegasus galaxy. By eliminating four partially grown ships that could have been used to attack Atlantis and hinder the evacuation ships as they hauled technology too big to fit through the stargate back to Earth, the odds of the Wraith succeeding in capturing Atlantis before the pullout had been reduced significantly.

The I.O.A. hadn't bought it and had thoroughly raked Sheppard over the coals. He had argued with them for over four hours but in the end they were going to get what they wanted regardless of the truth. He would be moved onto court martial and the far-off Atlantis command that had always been outside of their comfortable reach would be disbanded and destroyed…after they had ransacked the city for any and all valuable technology.

Sheppard was returned to his cell and dropped unceremoniously to the ground. He pulled his back up against the claustrophobic wall and cradled his head in his hands. He was screwed and he knew it. The SGC and his country were going to sacrifice him and the Pegasus galaxy to the corrupt whims of the I.O.A. for whatever deluded or twisted reasons they had.

Sheppard had dodged the bureaucratic bullet many times before, but not this time. He wasn't about to give up, but with his options being what they were, his thoughts were sliding more towards jail-break rather than the defense at his upcoming court martial.

* * *

"How are you feeling, son?" O'Neill asked Stevenson.

The Captain blinked his eyes open. "_Headache_."

"Don't bother talking, Stevenson," O'Neill said with a dismissive wave of his hand. "I don't speak Ancient anymore, and I don't feel like dragging Daniel in here, so just listen."

Stevenson nodded.

"I've deactivated the cameras so this will be a private conversation between the two of us," O'Neill said ominously, which drew a raised eyebrow from Stevenson.

"You're in hot water with the I.O.A., and I'm not sure if we'll be able to protect you. They look at you as a combination guinea pig/data file more valuable than…well, than anything they've come across to date, and in my opinion they're not going to give you up."

"I need to know if your head is as scrambled as mine was, or if you have control of the knowledge in your mind."

Stevenson raised his hands and smirked quizzically as if saying 'why.'

"If I can feed the I.O.A. some intel on my terms I can move you out of their reach to one of our more discrete offworld bases and dig my political heels in. So long as the information is flowing back to us I think I can protect you."

Stevenson shook his head 'no.'

"You don't have control?" O'Neill asked, disappointed but not really surprised. It had been a long shot idea from the beginning ten minutes ago in the commissary.

Stevenson shook his head 'yes.'

"Yes you agree with the 'no' or yes you can?" O'Neill asked confused.

Stevenson gritted his teeth then made a snap decision to trust O'Neill. He motioned for him to come closer.

O'Neill moved his chair up next to the head of his bed and leaned forward. "What?"

Stevenson reached out and touched O'Neill gently on the right temple. Stevenson's eyes glassed over and a host of images flooded into O'Neill's mind…and suddenly he understood.

Stevenson released the mental link and O'Neill sat up straight.

"Take Sheppard with you. He's in a holding cell down the hall. You've got two more days before he's taken away for court martial. Will that be long enough or do I need to buy you some more time?"

Stevenson gave him a 'thumbs up.'

O'Neill nodded and quickly left the room. He reactivated the security cameras and other recording devices then headed back to the commissary for an extra dessert. He found himself in a much better mood than before, with a hankering for banana pudding.


	6. Chapter 6

Sheppard was lying helplessly on his small cot behind the cell's bars when he heard a commotion outside and saw his personal guard jump out of his seat and run into the hall.

"Hey, what's going on?" he asked into the empty air.

Seemingly in response, his guard came back into the room flying through the air. He hit the far wall and slumped to the ground unconscious.

"What the hell?" Sheppard muttered.

Stevenson walked into the room wearing an oversized uniform and lifted a hand toward Sheppard's cell. The lock screeched and cracked open. The door swung free and Stevenson beckoned Sheppard forward with a simple hand motion.

"Okay…" Sheppard said slowly, not knowing what was going on but glad for the chance to get out of his cell none the less.

Stevenson pointed to the unconscious guard, then tugged on his own uniform.

"Right," Sheppard said, looking down at the orange jumpsuit that he was wearing. He knelt down next to the guard and proceeded to swap clothes with him. After he was finished he joined Stevenson at the door. "What next?"

The man muttered something in a language he couldn't understand, then, seeming to realize that fact, he drew a circle in the air then pointed through it.

Sheppard raised an eyebrow. "Stargate?"

Stevenson nodded.

Sheppard pointed out the door. "After you and your magic hand."

They moved quickly through the halls, with Stevenson telekinetically knocking aside a few personnel as needed. They passed by an armory and ducked inside briefly, grabbing some essential gear. Forty seconds later they were back in the hallway headed for the gateroom when the base alert siren went off.

"Let's move it," Sheppard urged, staying one step behind Stevenson.

A pair of armed guards stepped around the corner in front of them, ordering them to stand down. A split second later the guards were lifted into the air and clunked hard into the ceiling. Their weapons dropped to the ground a moment before their unconscious bodies did.

One of the Zats lying on the floor suddenly lept through the air and into Stevenson's hand. He tossed it back over his shoulder to Sheppard, who awkwardly caught it in mid-air.

When they reached the outside of the gate room Stevenson struggled for half a minute with the blast door before finally opening up a half-meter crack…just enough for the pair to slide through. He closed it behind them with a thud and swiped a bead of sweat off his forehead. He was expending a lot of his limited amount of energy…and he knew he had to get through the gate before he passed out again.

"How are we going to dial from down here?" Sheppard asked as General Landry's face appeared in the control room window.

"Colonel Sheppard, Captain Stevenson, stand down immediately. This is a direct order. We have assault teams moving on your position as we speak. If you resist they will be authorized to use force as necessary to return you to either the brig or the morgue. Your choice, Gentlemen."

"Doesn't look like I have much to lose at this point, General," Sheppard yelled back as he looked over his shoulder at Stevenson. "Please tell me you have a plan for getting out of here?"

Stevenson visibly gathered himself and set his jaw before stepping over to the side of the stargate. He reached out and touched it, then closed his eyes.

For a moment nothing happened. Then all of a sudden the computer readouts in the control room began showing erroneous feedback.

"Sir," Siler said from the control board. "We're reading a dialing sequence, but it's not originating from the control room. We're completely locked out."

"How is that possible?" Landry asked.

"I don't know, sir" Siler said apologetically.

"Pull the plug," Landry ordered.

"Too late," Siler noted.

The event horizon of the wormhole appeared, but without the customary kawoosh beforehand. Stevenson, looking exhausted, walked around and up the ramp, pulling Sheppard forward by the elbow.

He took the hint and followed him through the gate, but not before he paused, grinned, and waved a sarcastic goodbye to Landry in the control room.

* * *

Both men emerged into a clearing outside a wide, dark forest. Sheppard stopped just beyond the gate and looked around, trying to get a feel for where they were.

Stevenson, however, immediately went for the DHD. He touched the center bubble and closed his eyes. The gate shut down a few seconds later and he immediately started to dial another address.

"Smart," Sheppard said appreciatively. "They won't be able to follow us if we dial out again."

Stevenson nodded as the kawoosh from the newly formed wormhole jutted out into the blue, sunny sky.

"Come," Stevenson said awkwardly, as if he'd never spoken the word before.

"So you can talk? Sheppard asked as they stepped into the gate.

They emerged into a desert world with no one and nothing in site. Sheppard thought it looked a little familiar but he couldn't quite place the address.

"What now?" he asked, glad to be free again, but still unsure as to what was going on.

Stevenson pointed at the gate and started dialing another address.

"Again?" Sheppard asked. "They shouldn't be able to trace us this far."

Stevenson didn't answer. Instead he slowly input seven symbols…then he touched an eighth.

"DHD's can't dial another galaxy," Sheppard insisted. "They don't have enough power. Wish they could, then I could get back to Pegasus."

In response to his assertion the DHD began to light up randomly, as if it were having a motherboard meltdown. Stevenson input select symbols in response to the flashing lights for nearly a minute. Then all the symbols illuminated simultaneously and steadily. He reached up and pressed the center bubble and activated the gate.

"What the hell?" Sheppard asked.

Stevenson motioned him forward and led him through the gate...

Sheppard's jaw dropped when they emerged on the other side. They were inside a massive facility, obviously of Ancient design, but the most awe inspiring sight was the presence of four other gates sitting side by side with their own.

Sheppard stepped out and looked back up at the gate they had come through. "Holy crap…they're yellow," he said, referring to the chevron lights as Stevenson walked off into the distance.

"Hey, wait up!" he yelled as he looked back at the other gates. One had normal red crystals, while the others had blue, green, and orange chevrons.

Sheppard caught up with him just before he entered an alcove in the near wall that lead to an ascending staircase. He followed Stevenson up and through a latticework of hallways until they stopped before a thick, sealed door.

Stevenson waved a hand over a nearby panel and the 10cm-thick door slid into the wall. Sheppard followed him in and found himself in familiar surroundings. There were Ancient-style control panels, similar to those in Atlantis's gate room, ringing a center platform with a single podium on its perimeter.

Stevenson walked up to the podium and a holographic map materialized above the platform…identical in every way to its counterpart in Atlantis where he'd first seen a diagram of the Pegasus galaxy.

Sheppard frowned. The map didn't show the Pegasus galaxy, obviously, but it wasn't showing the Milky Way or any other galaxy either. He walked up alongside Stevenson's shoulder as he worked the controls, and with a closer look the significance of what he was seeing finally dawned on him.

"It's a map of the Ancients' galaxies," he said, half looking at Stevenson, but unwilling to take his eyes completely off the map. Out of the corner of his eye he saw the man nod in agreement.

"What is that, two, four, six…twenty two galaxies? That's insane! Where are we?"

Stevenson highlighted one of the central galaxies with a white hue.

"And where's Pegasus?"

Extra, colorless galaxies materialized around and within the cluster. One of these suddenly highlighted.

"What's that mean? Why isn't it part of the group?"

Stevenson worked his mouth around, then finally uttered, "New."

"New?" Sheppard asked. "That's right, Rodney said the Ancients built the Pegasus gates after they left Earth. I guess that puts the count at twenty three."

Stevenson shook his head and pressed another button.

All the little dots within the galaxies suddenly connected to each other in a mass of millions of tiny lines that blurred together into a reddish hue…except Pegasus, where there weren't even any dots, just a swirling mass of white.

"Not on the map, huh?" Sheppard speculated as another thought struck him. "Is that why we can't dial out of Pegasus without the Atlantis gate crystal?"

Stevenson rubbed his forehead and nodded. Apparently he was still feeling the fatigue from their escape.

"Don't supposed you can update the map?" Sheppard said offhand.  
Stevenson looked at him worried, then slowly nodded his head up and down, quickly followed by left to right.

"You can but you can't?" Sheppard tried to translate.

Stevenson pointed at the map and input a new command. For a long minute nothing happened, then all of a sudden a dozen or so dots appeared in Pegasus. Then a few more appeared, and more, and more until the entire galaxy was full of new stargate locations.

"Does that mean we can dial Pegasus from here?"

Stevenson pointed at the map again…more specifically at the lines interconnecting gates within and between galaxies. None traveled to Pegasus.

"Not hooked up, huh?" Sheppard guessed. "Can you fix that?"  
The Captain reached a hand up to Sheppard's chest and pushed his palm flat against it in a feeding motion.

"Don't want to let the Wraith out, I get it. Any way we can still get there? Unless you have somewhere else for us to go?"

Stevenson held up a finger, giving Sheppard the 'wait' signal. Suddenly the map zoomed in on the Milky Way galaxy alone, and for the first time he could see that the lines connecting the dots were different colors.

He glanced out the window at the different colored stargates on the platform below them and raised a curious eyebrow. "Where are we?"

Stevenson highlight and zoomed in on one small dot near the galactic core. Sheppard noticed that lines of all six colors intersected it. He frowned. There had only been five gates, and none of them purple.

"Where's the purple gate?" he asked Stevenson while pointing at the mass of thin colored lines emanating from their location to what looked like every other stargate in existence. It was hard to differentiate them all, but the colors stood out.

Stevenson pulled up a holographic diagram of them in the control room and zoomed outward through the massive complex.

"We're in space?" Sheppard realized as the diagram resolved itself into a space station with another gate floating outside.

Stevenson nodded 'yes' to his question and highlighted the gate.

"Wait a minute, how big is this station?"

Stevenson brought up a second diagram of an Atlantis-style city for comparison, which overshadowed the complex at approximately twice its size.

"If I'm reading this right, then that gate," Sheppard said, pointing to the one in space, "is a supergate?"


	7. Chapter 7

Stevenson nodded and highlighted all the purple dots within the galaxy. Sheppard saw a hundred or so locations strategically spread throughout various sectors.

A connection clicked in his mind. "That's why the Ancient warships didn't have fast hyperdrives. They didn't need to go very far to get to the sector gate. Probably faster to get across the galaxy this way than to travel all the way using hyperdrive…where's Earth?"

The purple dots faded back to normal and another dot further out from the galactic center brightened and enlarged. Only red lines intersected it.

"Did all that stuff you did on the DHD have anything to do with these colored lines and the different color stargates?" Sheppard hazarded a guess.

Stevenson nodded.

The Colonel's pulse spiked. He had a feeling he was onto something big. "Are the gates different from each other?"

He nodded again.

"Twenty questions then…do colors only connect to similar colors?

Again, a 'yes.'

"We came through a red and exited from a yellow, right?"

Stevenson nodded and pulled up a diagram of two gates and a DHD that superimposed over the galaxy map. Both gates glowed red and a red line connected them. They disappeared and reemerged as a red and a green without a connection.

"Ok, different colors don't connect. I get that. So why did we come out a yellow when there was a red a few steps away?"

The DHD suddenly showed seven symbols highlight. Stevenson tapped a button and an 8th illuminated. When it did the red gate changed colors to green and a connection formed between the two gates.

"Damn, I wish Rodney were here. Ok, so you can change the gate's color with the DHD?"

Stevenson hesitated, rolled his eyes in helplessness, then reluctantly nodded 'yes.'

"What was that look for?"

Stevenson pointed at the gates outside, then did an amicable job of forming the shape of the gate crystals with his fingers.

"The gates…colors?" Sheppard guessed.

He nodded, then pointed back to the faint dots in the galaxy map.

"I'm sorry, I don't get it."

Stevenson blew out a frustrated breath and reached a hand up to Sheppard's temple. A moment later the Colonel suddenly understood and the Captain looked even more exhausted than before.

"Neat trick," Sheppard said, a bit impressed and creeped out at the same time. "So the crystals don't actually change colors, but the gates act like they're a different color.

Stevenson nodded, relieved.

"So why didn't we come in through the red gate?"

Stevenson pointed at his chest and shook his head 'no.' He pointed away from himself and shook his head 'yes.'

Sheppard glanced back at the gates for a second before catching on. "You can dial out, but not in? Some type of security precaution?" Sheppard guessed and Stevenson confirmed with a tired nod.

"So we got here by switching colors, which you managed with the extra symbol on the DHD. I thought that was for dialing another galaxy."

Stevenson again nodded.

Sheppard frowned. "How can it do both?"

He held up nine fingers in response.

"Ninth chevron?" Sheppard said as his jaw dropped. "It moves us between different color gates?"

Another nod.

"But you only input eight chevrons?"

Stevenson used the DHD diagram and input the standard six symbols, then the point of origin, then the activation bubble in the center. A line connected the two stargates, both of which had been reset to red before he began.

He held up a finger to forestall another question and input the standard six symbols again, then a seventh, then the point of origin. The gates connected and a galaxy to galaxy line appeared.

"Intergalactic," Sheppard noted.

The two gates switched to one red, one green. Stevenson reinput six commands, the point of origin, then another symbol before hitting the activation bubble.

The two gates connected when the green gate turned red. Stevenson pointed to the point of origin icon in the string of eight symbols hovering just below the DHD.

"It comes after the point of origin," Sheppard said, catching on. "That's why it doesn't dial intergalactic."

Stevenson reset the diagram one more time with one red gate and one green gate. He input six icons, then belatedly a seventh, then the point of origin, then the ninth chevron before finally the activation bubble.

The green gate turned red again, but this time the intergalactic connection showed up again.

"Eight for in-galaxy gate-jump, nine for intergalactic gate-jump?" Sheppard asked, feeling like a stargate rookie getting his orientation lesson. And to think, the SGC and the IOA thought they had a complete list of every stargate within the galaxy. The Ancients had far better security than he'd ever given them credit for.

Stevenson nodded curtly, apparently satisfied, and turned back to the map. He got rid of the diagram and input some new commands. Another long pause ensued while the computer worked on something.

"What was with all the flashing symbols when you dialed?"

Stevenson held up his forearm and started tapping on his wrist, pretending he had a GDO.

Sheppard raised an eyebrow. "Some kind of access code?"

Stevenson nodded as a few of the dots on the map began to disappear.

"Dead gates?" Sheppard guessed.

He nodded regretfully. Once the system completed the update, Stevenson scrolled through a list of planets and found the one he wanted. It was listed as having a green stargate only, and suddenly the green gate outside the window flashed to life, but without the corresponding kawoosh. The event horizon just popped into place.

"We moving on?" Sheppard asked, adjusting the pack on his shoulders.

Stevenson held up the wait finger again.

A picture materialized over the galaxy map, revealing another large chamber with ancient-looking tech. This one had numerous struts extending from floor to ceiling with what looked like workstations spread around their bases.

"Are we seeing that through the gate?"

Stevenson nodded.

"Did you send a probe through?"

Stevenson shook his head 'no' this time. He made the stargate circle symbol with his finger.

"The stargate? Wait a minute, are you saying the stargates have a camera in them?"

Stevenson turned to look at him and nodded an ironic 'yes.'

"Why the hell didn't Rodney find that? Ah…of all the times we needed intel about what was on the other side of the gate we had the perfect tool right under our nose!"

Stevenson motioned to Sheppard to come with him as he headed for the door.

"Guess we're going."

They wound their way back through the maze of hallways and down the staircase. When they got to the green stargate it was still open and Stevenson walked through without preamble. Sheppard followed close behind, glancing up at the green crystals just before he passed through.

They both emerged on the other side into what Sheppard immediately guessed to be some factory. He didn't have any hard evidence to back that theory up, but the congestion of equipment and lack of windows gave it that feel to him.

Stevenson quickly found the control panel he wanted and suddenly the entire facility hummed to life with a restored power flow. He brought up a display screen and a list of data. He highlighted several sections and hit an overly large button on the control panel in front of him.

Sheppard glanced over his shoulder as the machinery started to activate, doing what he couldn't imagine. "What is this place?"

Stevenson motioned for him to follow, and together they worked their way through the now active facility into a storage depot on the opposite side of the complex. Inside Sheppard saw small, empty racks lining the walls and partitions.

"What are these for?" Sheppard asked.

Stevenson reached into the one and only occupied alcove in the depot and pulled out a ZPM.

"No way!" Sheppard said in utter shock.

Stevenson held up two fingers.

"Two? Where's the other one?"

Stevenson pointed out into the center of the facility.

Sheppard glanced out the door, then back to the numerous empty racks. "Does this place make the ZPMs?"

Stevenson smiled…and nodded 'yes.'

Sheppard fist-pumped the air. "Now that's what I'm talking about."

The Captain smiled and motioned for him to follow. He led him back to the gate and reactivated it. Sheppard glanced back at the active machinery. "How long is it going to take to make another?"

Stevenson made a looping motion with his outstretched finger.

"A while," Sheppard translated as he followed Stevenson back through the gate.

When they got back to the 'gate center', as Sheppard thought of it, he noticed that they'd come back through the yellow gate again, not the green gate that they'd left through. He guessed yellow had a higher security rating than green, and followed the Captain back across the open platform to the wall alcove and the stairway to the control room.

Instead of going back there Stevenson led him further into the facility and into what looked like personal quarters. They both pulled some rations out of the packs they'd grabbed from the SGC armory and stretched out on the low beds. The cushioning had long since deteriorated, but the solid slab that was left proved adequately relaxing.

Stevenson finished his rations and laid down in a meditative pose. He remained motionless for the following six hours, in which Sheppard sat with his back against the wall, relishing his regained freedom and the awesomeness of where he currently was.

After soaking it all in he finally managed to fall asleep.


	8. Chapter 8

When Sheppard woke up ten hours later he found Stevenson's bed empty.

"Now where did he go?"

He stood up from the low bed and grabbed at his soar back. Sleeping on a stone slab was as bad as it sounded. After stretching a bit he ventured outside the door and tried to get some sense of where Stevenson had gone.

With neither a sight nor a sound to go by, he decided to backtrack to the command center…and found Stevenson once again at the holographic controls.

"There you are…don't go wandering off like that."

Stevenson glanced over his shoulder and said something in Ancient.

"Apology accepted," Sheppard said, guessing as to the context. "What have you been up to?" he asked as he glanced out over the multi-galaxy map again. There seemed to be fewer dots amongst the other galaxies this time…but a number of interconnecting lines within Pegasus had been added, but without any extragalactic lines. There were, however, a few dots in between galaxies that he guessed were the remains of the gate bridge.

"What happened here?" he asked, pointing to Pegasus. "And what is that?" Sheppard added, noticing another new galaxy far outside the Ancients' territory. It was connected to the Milky Way by a solitary gray line.

Stevenson made the symbol for stargate with his finger.

"Stargate." Sheppard said.

Stevenson formed an 'O' with his fingers and expanded it outward.

"Bigger…you mean supergate?"

He nodded and pointed at the two ends of the gray line.

"That's the Ori galaxy?" Sheppard asked.

Stevenson gave him a thumbs up.

"You can tap into their network from here?"

The Captain held his hand up and wiggled it.

"Kind of…partially?" Sheppard guessed.

Stevenson held his fingers up and pointed at his eyes and then at the supergate connection.

"See…you can see it? You can detect it?"

Another thumbs up.

"But you can't control it?"

Stevenson shook his head 'no.'

"What about Pegasus, can you control their gates?"

Thumbs up again.

"Can you get us back there?"

He nodded and held up two fingers…then three.

"Two, three," Sheppard repeated. "Two what?"

Stevenson held his hands about a foot apart, one above the other.

"ZPM? Two ZPMs plus the one in Atlantis make three? That's what they're for?"

Another thumbs up.

"Then what? The I.O.A. and stargate command still control the city. We go there and we'll get sent back to Earth."

Stevenson shook his head 'no' and reached out to Sheppard's temple again. A moment later he released him, his eyes wide with surprise.

"That…could work," were all the words Sheppard could manage in total shock.

* * *

"Caldwell to Atlantis, we're ready to beam aboard the second shipment now," the _Daedalus_'s commander said over the intercom in Atlantis's gateroom.

"Woolsey here. You have clearance to proceed," he said, referring to the second load of scavenged tech from the city that was too large to fit through the gate and take back to Earth the easy way.

The _Daedalus_ activated its beaming technology and started plucking specific items from Atlantis's various wings while Woolsey continued to oversee the stacking of smaller crates on the gateroom floor in preparation for the next direct connection back to Earth.

Once they'd managed to strip the city of everything remotely useful, the _Daedalus_ or _Apollo_ would bring five gate-buster nukes back from the Milky Way and beam them into the city as a means of obliterating the remaining superstructure. The gate link back to Earth would be destroyed as well as what was left of Atlantis's hyperdrives, forever stranding the Wraith in the Pegasus galaxy…at which point Earth would wash its hands of the whole affair while reaping the plunder from the lost city and preserving the finite remaining power in the ZPM.

"Incoming wormhole," someone shouted from behind Woolsey.

"Who could that be? We don't have any teams off world," Atlantis's commander asked.

"We're receiving no IDC, sir."

"Keep the shield up," Woolsey warned. "It could be the Wraith…or god knows what else," he uttered just before the shield dropped, exposing the incoming wormhole.

"I said keep the shield up!" he yelled, glaring at the tech sitting at the dialing station.

"It wasn't me, sir. My controls are being overridden. I can't raise it again!"

"Security to the gateroom!" Woolsey yelled in panic as he started to backtrack from the open gate. "Find out where that override is coming from and some way to get around it."

"What's going on?" Teyla asked as she ran into the gateroom.

"We don't know and we can't raise the shield," Woolsey explained.

"John!!!" she suddenly exclaimed as Sheppard and Stevenson walked through the gate.

"What the hell?" Woolsey said as he darted back down the stairs. "Why did they send you back? Aren't you supposed to be awaiting court martial?"

"Sheppard!" Ronon yelled excitedly as he entered the gateroom a few seconds behind Teyla.

"Hey buddy, good to see you."

"Answer me, Colonel," Woolsey insisted as they walked up face to face in front of the gate.

Before Sheppard could smart off, Stevenson reached his hand out and the control pillar shot up from the floor. He placed his hand on it and suddenly the lockdown alarm sounded.

"What the hell is going on?!" Woolsey demanded. "Security!"

Four SF's stepped forward and raised their guns on the pair while another three started to come down the staircase.

Stevenson raised a hand and ripped the guns away from the nearest two. A split second later Sheppard pulled out his Zat and shot one of the others. Ronon got the fourth with a quick draw before the man could fire at Sheppard.

The three coming down the staircase quickly took fire from both Sheppard and Ronon while Stevenson relieved another of his weapon. Within seconds the gateroom was back in their hands.

"Thanks buddy," Sheppard said to Ronon as he trained his Zat on Woolsey.

Stevenson, meanwhile, darted up the stairs and ran to the city control board and raised the city's shields.

"Are you insane? Who is he?" Woolsey asked almost simultaneously.

"He stuck his head in an Ancient microwave and got superpowers," Sheppard said sarcastically as Woolsey's radio buzzed with static.

"_Daedalus_ to Atlantis, why did you raise shields?" Caldwell asked, quite miffed.

"Ronon, Teyla, keep them under guard," Sheppard ordered as he bounded up the staircase.

"Move," he told the tech at the dialing station.

The man slid out of his seat while Sheppard dialed Earth.

"What's going on?" Teyla asked, very concerned.

"We're not going to let Atlantis be destroyed," he answered bluntly. "And we're not going to abandon the Pegasus galaxy either."

"And by us you mean?" Teyla asked.

"By us I mean me and my new best friend."

"And he is?" she asked, frowning.

"Captain Stevenson," Sheppard answered. "He can't talk but he can still hear us just fine."

"Wait a minute," Ronon asked, "the two of you are planning to take over Atlantis on your own?"

Sheppard glanced over at Stevenson, who gave him a nod of confirmation as he continued to work the controls. "Actually, we already have."

"Who'd you get to lower the shield for you?" Woolsey asked snobbishly. "McKay?"

"Nope, he did," he said, pointing to Stevenson.

"How?" Woolsey asked incredulously.

"None of your concern," Sheppard said as he sent Atlantis's IDC signal through the gate. He jogged back down the stairs and snatched the radio from Woolsey's shoulder, cutting off Caldwell's continued questions with a quick flick of the switch. He grabbed Woolsey by the collar and dragged him up to the gate.

"Here's the deal. I'm kicking your butt back to Earth first so you can tell them not to raise the iris the next few times we dial in. I'm going to give everyone on Atlantis a choice to stay or go. Those who want to go, and those I can't trust, will be sent back through the gate to Earth, at which point we're cutting all ties with the I.O.A. and anyone under their command."

"You're insane," Woolsey said slowly. "You'll never get away with this."

"We'll manage," Sheppard said before using the business end of his boot on Woolsey's butt, knocking him through the event horizon. "Send the guards through," Sheppard ordered Ronon and Teyla.

Ronon responded immediately, but Teyla hesitated. "Colonel, are you sure you know what you're doing?"

"Too late too turn back now if I wasn't," he said sarcastically. When she didn't move he looked her in the eye and confidently said, "Yes."

She nodded that that was good enough for her and started to drag one of the unconscious guards toward the gate.

"How are we doing?" he asked Stevenson.

The Captain pointed to the comm button.

"Alright, here goes nothing," he said, placing his hand on the panel and activating the city-wide intercom.

"Everybody listen up. This is Colonel John Sheppard, acting commander of Atlantis. I've taken control of the city and initiated a comprehensive lockdown, so just sit tight for a while, you're not going anywhere for a couple of hours."

"In my opinion both the I.O.A. and stargate command have crossed the line when they decided to abandon the Pegasus galaxy to the fate of being Wraith food…not to mention destroying Atlantis in the process, but only after stripping it down like a pack of lowly scavengers. I would like to think Earth is better than that, but recent events have shown me otherwise."

"I, however, am not going to abandon Pegasus, nor am I going to let the city be destroyed. I've already been declared an enemy of Earth, if not I will be soon, so I don't have the luxury of going back…but you do. So you have a choice to make."

"Anyone that wishes to stay here and fight the Wraith will be welcome to, but it will mean never returning home to Earth, as well as imprisonment if we were ever captured."

"I know this is a lot to throw at you all at once, but you're going to have some time to think it over as long as the lockdown is in effect, so think hard. You won't get a chance to change your mind…either way. If you choose to go back I won't hold it against you personally. I'll understand if you can't bring yourself to turn against Earth…me, with a court martial waiting back home, it's an easy choice. For you I know it won't be."

"Talk amongst yourselves, think it through. Contact the gateroom over the comm when you finally decide, or wait for us to come around room by room. Figure a couple of hours at least. Sheppard out."

Teyla and Ronon joined Sheppard on the command platform as the gate finally shut down. "I assume you two are with us?"

"We were staying behind anyway," Ronon pointed out.

"Just checking," Sheppard added. "What about the rest of you. Anyone want to turn renegade?"

The half dozen people in the control room exchanged glances and bashfully shook their heads 'no.'

"Ok," Sheppard said, expecting as much. "Redial the gate, check with the SGC to make sure the iris is down, then head on back."

"What about our personal belongings?" one of the techs asked.

Sheppard glared at him and the man held up his hands in defense. "Never mind."

"Teyla, watch over the gateroom and make sure they get back safely. We'll be sending more this way," Sheppard said as Stevenson headed for the door. "Ronon, come with us. We'll need help with security."

Ronon brandished his weapon. "Gladly."


	9. Chapter 9

Five and a half hours later the last wormhole to Earth was opened. Most Atlantis personnel had left without incident, but a few SF's had to be physically subdued. The last group of those not willing to stay walked through the gate, leaving Sheppard, Teyla, Ronon, and Rodney standing in front of the portal back to Earth.

"I'm sorry," McKay said for the fiftieth time.

"I understand, Rodney," Sheppard said, placing a hand on his shoulder. "You've gotta do what you've gotta do."

"It's not that I don't want to stay, but I can't live with the thought of never seeing Jennifer or my sister again. But then again I don't want to abandon you guys either…despite the fact that you have zero chance of pulling this off, and with me staying you'd at least have a small chance of staying alive…"

"Rodney," Sheppard interrupted. "It's ok. Go."

McKay wanted to say something more, but couldn't find the words. He stepped forward and hugged Sheppard, who returned the gesture without hesitation or complaint.

Teyla came forward, hugged him, and even gave him a peck on the cheek. "Goodbye Rodney."

Ronon starred down McKay when he approached him with intent to hug, then softened and dragged Mckay over, lifting him up off the ground in a giant bear-hug. "Take care."

McKay looked back at all of them, trying to find the right words. "Good luck," he said simply, stepping slowly, reluctantly through the gate.

Sheppard swiped a tear from his eye and walked back up to the control platform. He pressed one of the comm buttons. "You're a go, Stevenson."

* * *

Across the city, sitting in the Ancient control chair, Stevenson heard Sheppard's voice and leaned back, closing his eyes in concentration.

The city rumbled through the pre-flight activation of the stardrive. Sheppard, Teyla, and Ronon waited in the gateroom and watched the city lift off from the ocean effortlessly, thanks to the three ZPM's now powering its engines. The handful of other personnel that had decided to stay watched the liftoff from various points around the city, wondering silently if they'd made the right choice.

The city continued up into orbit, passing the helpless _Daedalus_ by and entered hyperspace without incident.

"Helm," Caldwell called out on the _Daedalus_'s bridge, "track them and lay in a pursuit course."

"Sir," the helmsman answered, "Atlantis will be out of sensor range in three minutes. They're traveling far faster than the _Daedalus_'s engines are capable of."

"What?" Caldwell asked. "How is that possible?"

"I haven't a clue, sir. But there's no way we can follow them at these speeds."

"Plot their current trajectory at least," Caldwell insisted.

The other bridge officer consulted his control screen. "At present they're heading leads them to…intergalactic space."

"Back to Earth?" Caldwell guessed.

"No, sir. Above Pegasus's galactic plane…into the middle of nowhere."

Caldwell rubbed his chin for a moment. "Helm, set course back to Earth. We need to consult with stargate command before we proceed any further."

* * *

Atlantis sat in intergalactic space overlooking the Pegasus galaxy, its precious atmosphere safely contained within the city's shield. Sheppard, Teyla, and Ronon gathered in the mess hall, discussing the implications of what they had just done, much as everyone else on Atlantis was doing at the moment…all save one.

Stevenson was still on the move, and had been ever since he'd left the chair room. Currently he was in the holo-room going through the updates to the Ancient database that had occurred since the construction of the Repository of Knowledge. He knew far more about the Ancients than any living person, but the Pegasus Ancients were a complete mystery to him…hence he had a lot of catching up to do before he started to tackle the challenges ahead of him.

"_Are you in pain?_" a voice from behind him spoke in Ancient.

"_Yes, but I'm managing_," Stevenson said, turning around to face the ascended Ancient.

"_I apologize for the discomfort that you must endure, but I could find no other way. Your body is in a constant state of flux, and will remain so for quite some time…until your advancement reaches a level where you can defend yourself from ascended beings. Once you reach that point you will have a choice: let the changes plateau or push on further_."

"_And if I continue on?_" Stevenson asked.

The image of the Ancient man shrugged. "_We don't know. No one has ever been allowed to develop that far._"

"_Tell me about the others. You must have learned more over the past few million years?_"

The Ancient's expression tightened. "_Yes...they're not all ascended beings, as we first believed. The core of the Ascended Empire is made up of a nameless race of energy-based lifeforms. They are the ones who have forced the assimilation of ascended beings into the Empire, and they are the origin of the non-interference and limited development edicts. They have a distaste for corporeals and, I think, they also don't want us interacting with our previous species_."

Stevenson raised an eyebrow. "_How many other species are we talking about?_"

"_Hundreds, if not thousands. Humans are one of the newer additions to the group. We're discouraged from information gathering, I think the Originals, that's what we refer to them as, like to keep us in the dark as much as possible. We have surmised that the Empire's domain extends through several hundred galaxies but, ironic enough, seems to end somewhere between Avalona and Destra._"

"_Really_," Stevenson remarked, "_the Ori weren't part of the Empire?_"

"_Oddly enough no, though they were closely monitored to determine if they would ever become a threat to the Empire. They knew that if they ventured into the Originals' domain they had to operate under their rules, but as long as they stayed outside of their territory and posed no threat to them, they were essentially free to do as they pleased_."

"_Interesting. Why didn't you and the others leave their domain?_"

The Ancient sighed. "_Once part of the Empire, forever are you bound to it. A few of us tried to leave and were tracked down by the others. Some returned...those who didn't were killed_."

"_Are you in danger talking to me?_"

He shook his head. "_The Universe is a big place, the Originals and their followers can't watch over everything. Some of the Alterra have, regrettably, assimilated into the Empire and assist them in watching us. I've been given a short window of time to meet with you while a few loyal Alterra distract them. It is doubtful I'll be able to consult with you again without drawing you unwanted attention_."

Stevenson nodded. "I _understand. What else do I need to know?_"

"_My name is Lyran. I'm the one who developed and added the secondary programming to the Repositories…with the help of a few non-ascended Alterra before they finally died of the plague. I wasn't allowed to help them ascend and was forced to watch them die helplessly. To make matters worse, I've also discovered that it was the Originals who created the plague. They deemed us too dangerous and decreed that we could not be allowed to advance any further. They are also the ones responsible for killing the Asgard by tampering with their DNA and causing their gradual deterioration…as well as their inability to ascend._"

Stevenson's hands balled into fists. Blood dripped from where his fingernails were cutting into his skin. While he might not have been blood kin to the Ancients, the changes the Repository had made to his body and mind had essential turned him into one of them…and he found himself taking the news of their murder personally.

"_Now you understand how far they will go to insure that no corporeal species will ever threaten them. They also have to limit the number of new ascensions for fear of us one day outnumbering them. They tolerated the few of us that ascended, but made sure that no Asgard would, given our former alliance. The Originals and their Empire are not to be trifled with. You must be very careful, and very patient. Once you show your hand we won't get a second chance at this_."

Stevenson nodded slowly. "_I plan to stay here and deal with the Wraith while I develop. What of the Furlings?_"

Lyran shook his head. "_I would not involve them so soon. They are still in Ryss and Nextor, and have yet to attract the attention of the Empire. Do not involve them until you are in a position to protect them_."

"_I'll keep that in mind. At least they're still alive_."

"_Alive, but at risk. They are currently involved in a war of their own against an enemy far more powerful than the Wraith. Don't get involved in their fight until you're ready_."

"_What can you tell me of the Wraith? How did they defeat the Lanteans?_"

Lyran glared with contempt. "_The Lantean civilization was too focused on developing to the point of ascension. They lost the war out of pure stupidity. If you use the technology available to you wisely, you should have no trouble defeating them_," Lyran said, glancing over his shoulder. "_I must go. Good luck, brother_."

Lyran faded from view, leaving Stevenson alone in the holo-room. He wiped his bloody palms off on his pants, revealing smooth skin beneath…his cuts had already healed.

He took a moment to gather his thoughts and get his emotions back in check, then he returned to his search through the database. He couldn't afford any missteps with the Wraith out of ignorance. It could jeopardize everything.


	10. Chapter 10

"Excuse me for saying so," Teyla interjected from her seat in the briefing room, "but I find it hard to believe that the few of us that are left on Atlantis would have any chance of defeating the Wraith."

Sheppard glanced at Stevenson, then back at Teyla. "We do have our own Ancient now."

"Yes, I noticed," Teyla countered, "but we've lost all support from Earth. No ships, no weapons, no soldiers…and no food."

Stevenson jutted a thumb at his chest.

"I think that means he's got it covered," Ronon speculated.

Teyla raised an eyebrow. "How, exactly?"

Stevenson opened the case lying in front of him on the table. He pulled out a small vile with gray dust inside.

"Nanites!?" Teyla exclaimed.

"You mean replicators?" Sheppard asked, stunned. "That's an insanely bad idea."

Stevenson shook his head. "Toooollls," he said, not quite getting the pronunciation right.

"Wait a minute?" Ronon said, leaning forward in his seat. "Are you saying we can use those things to build whatever we need?"

Stevenson nodded.

"Cool," Ronon decreed. "Why didn't we think of that earlier?"

"Because replicators have a habit of not taking orders," Sheppard said. "I'm hoping these are different somehow?"

Stevenson nodded emphatically.

"I'm wondering," Teyla added, "is this how the Ancients originally built Atlantis?"

Stevenson rotated his hand side to side in front of him.

"That means 'sort of,'" Sheppard translated. "Good enough for me, as long as you know what you're doing," he said, glancing at Stevenson.

"Do you mean to involve the humans in this galaxy in our fight," Teyla asked both Sheppard and Stevenson, "or do you intend to build an army of replicators to fight for us?"

"I…had expected to bring volunteers here and begin training them," Sheppard said hesitantly. Stevenson nodded his approval. "As for using replicators, you already know where I stand on that."

"But does he?" Ronon asked.

All eyes fell on Stevenson.

He reluctantly pulled out a datapad and meticulously typed in a message. He slid it across the table in disgust at his own inability to communicate, temporary as it may be.

"What did he say?" Teyla asked when John didn't immediately say anything.

"Seems he isn't opposed to using the technology, but he doesn't like the way the Lanteans built them to fight their war for them. At the least he intends to build some to use for security in Atlantis…" Sheppard said, shaking his head. "I am not going to agree to that…unless you can 100% assure me that what happened the first time isn't going to happen again."

Stevenson motioned for the datapad back. He typed a quick message, then returned it.

"Lanteans were stupid," Sheppard read aloud for the others to hear. "They programmed them to be autonomous and aggressive. Ours will be neither."

"Forgive my bluntness," Teyla interjected, "but if you have the replicators, what do you need humans for?"

"Good point," Ronon added.

"Much," Stevenson said, almost normally.

Teyla raised an eyebrow. "Like what?"

Stevenson retrieved the datapad again. This time he slid it to Teyla when he was finished.

"He says that machines can only do what they're programmed to do. They can't think for themselves, they have no sense of right and wrong. They are only tools. Nothing more."

Teyla placed the datapad back on the table, already feeling better about Stevenson. "I agree, and my people will be willing to help as they can."

"Good to know," Sheppard said, pleased. "Ronon, how do you feel about training ourselves an army to fight the Wraith?"

The Setidan smiled. "About time."

"Alright then," Sheppard said, standing, "Stevenson, get over to the control chair. We should be exiting hyperspace soon and I don't trust myself to put the city down in one piece over land."

Stevenson stood, gave him a thumbs up, then left the room.

"This whole not talking thing is starting to get annoying," Ronon said after he'd left.

"It is a little weird," Sheppard admitted, "but he doesn't have a choice. His mind was reprogrammed to speak Ancient the same way General O'Neill's did. I'm just glad he can understand us."

"Perhaps he'll be able to relearn to speak normally again," Teyla suggested. "He has managed a few words."

"It's either that or he gets to carry a blackberry around the rest of his life," Sheppard said sarcastically as they left the briefing room.

* * *

Forty three minutes later Atlantis emerged from hyperspace back inside the Pegasus galaxy. Stevenson immediately started to bring them down from orbit over an ice world.

"This is Sheppard. Everyone hold tight, we're going in."

Stevenson slowed the city's descent rapidly, coming to a virtual stop over a rocky ridgeline jutting up through the kilometer-thick ice. Utilizing the city's engines and the power of all three ZPMs, he drifted Atlantis to the east until they passed over a vast ice field. Atlantis stopped over the smooth surface and began its final descent.

Sheppard had to catch his balance as the city shook violently as it punctured the ice sheet. The city's great weight drove the lower sections deep into the ice until they'd hollowed out a sufficiently wide cradle to support the city's weight. With one final tremor Atlantis imbedded itself into the ice field, riding slightly higher above the surface than it had in the ocean, but its orientation was still exactly parallel to the ground…a testament to Stevenson's piloting ability. Sheppard doubted he could have put her down with such accuracy, but he wasn't about to say that out loud.

It took about an hour for Stevenson to get the city tucked in and reestablish their connection to the gate network. Now that they'd switched planets and addresses, it was unlikely that Earth would be able to find them again…if they were going to look for them at all.

Sheppard wasn't sure what they would do. They had wanted out of Pegasus pretty bad, but now that he'd stolen Atlantis from them they were sure to be pissed…he just didn't know how far they'd go to come after him and the others who'd chosen to go rogue.

And he really didn't like the idea of having to throw down against their own battlecruisers, but he knew that was a distinct possibility.

At least their new location would buy them some time to get organized and regeared for their self-proclaimed war against the Wraith. Sheppard still had no idea how they were going to fight that war, but Stevenson had been adamant that they could win without assistance from Earth, and after what he'd shown Sheppard in the Milky Way, he was eager to see how this was going to play out.

To that end Stevenson brought Sheppard to an obscure wing of the city where he had been spending the past several hours since landfall. Two large, clear containers were three quarters full of dust-like nanites…with a small, steady stream of the gray particles being added to each as they looked on.

"That's…a lot of nanites," Sheppard commented. "Are those the security replicators?"

Stevenson shook his head 'no' and stepped over to a control panel where he brought up a map of their current location. It rotated until they could see both Atlantis and several kilometers beneath the surface of the planet. The Captain highlighted several deposits of naquada and neutronium in close proximity to the city.

"Mining," he said, again managing a word in English.

"Cool," Sheppard said as Stevenson stopped the inflow of new nanites. The two canisters disappeared downward into the floor.

"Where are they going?"

Stevenson brought up another schematic that showed the canisters being moved down a shaft to the underside of the city. From there they would be released into the ice and work their way down into the bedrock, building micro-conduits as they went that would funnel the raw material back up into Atlantis.

Stevenson handed Sheppard a case of viles and a datapad.

"What's this?" he asked. He looked at the screen and found it to be another translation.

**Take the canisters and release the contents on the following worlds. They are preprogrammed to activate ten seconds after the seals are broken. Don't open them until you are in position.**

**These nanites will begin gathering other materials we need and will report back to Atlantis via subspace.**

Sheppard glanced down at the two dozen addresses listed below the message and was suddenly glad for something to do other than follow Stevenson around.

"Will do," he said as he picked up the case and left Stevenson to his work. He radioed Teyla and Ronon and had them meet him in the gateroom.

"What are those?" Ronon asked.

"Our cargo. We're going to make some deliveries," Sheppard told him while signaling the sparse control room staff, made up of mostly Athosians, to dial the gate.

"About time we had a mission," Ronon remarked. "We've been sitting on our butts for too long."

"I agree," Teyla said. "It's time we got back to work."

Sheppard smiled as the kawoosh retreated back into the event horizon. "It's good to be back," he said as the three stepped through the gate together.


End file.
